[gmx-users] Error message while running energy minimization

[Deep Bhattacharya]

Hello,

This is the error message that I am getting trying to run energy
minimization

NOTE 2 [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

em.mdp

; minim.mdp - used as input into grompp to generate em.tpr
define       =  -DPOSRES -DPOSRES_LIGAND
integrator = steep
emtol = 1000.0
emstep      = 0.01
nsteps = 500000
energygrps              = System
nstlist    = 1
rlist               = 1.4
ns_type    = grid
coulombtype    = PME
rcoulomb    = 1.4
vdwtype        = cut-off
rvdw    = 1.4
pbc    = xyz
epsilon-rf     = 61

Please help

*Deep S Bhattacharya*

*Graduate Research Assistant*

Mohs Biomedical Imaging & Nanotechnology Group

Pharmaceutical Sciences

*University of Nebraska Medical Center*

4018 Eppley Science Hall  |  Omaha, NE 68198-6805

office 402.559.4349  | cell 402.906.1640

deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com